MyNutRiceBase is a repository of genomics and genetics information for rice nutritional traits by providing genome and transcriptomic data mining, visualisation (JBrowse) as well as sequence similarity searching analysis (BLAST) for the pigmented rice varieties. MyNutRiceBase integrates the variation (SNPs) with genes and pathways. MyNutRiceBase aims to accelerate genomics and genetics analysis by enabling researchers and breeders to mine and export the information for the application in the rice breeding programme, towards the improvement of nutritional traits in rice varieties.

Collaborators:

  • Centre for Marker Discovery & Validation (CMDV), MARDI (Mohd Shahril Firdaus)
  • Paddy & Rice Research Centre (RI), MARDI (Asfaliza Ramli)
  • Paddy & Rice Research Centre (RI), MARDI (Rahiniza Kamaruzaman)
  • Paddy & Rice Research Centre (RI), MARDI (Shamsul Amri Saidon)
  • Paddy & Rice Research Centre (RI), MARDI (Mohamad Najib Mohd Yusof)
  • Paddy & Rice Research Centre (RI), MARDI (Hanisa Hosni)
  • Rice GenebankTM, MARDI (Site Noorzuraini Abd Rahman)
  • Institute of Systems Biology (INBIOSIS), UKM (Zeti Azura Mohamed Hussein)

Frequently Asked Questions (FAQs)

What data and information does MyNutRIceVar contain?

The current data in MyNutRiceBase are:

  1. Reference transcriptome built from the assembly of 4 pigmented and two white rice varieties.
  2. Biosynthetic genes from the flavonoid and folate biosynthetic pathways.
  3. Co-expressed genes involved in the flavonoid and folate biosynthetic pathways.
  4. A Panel of putative SNPs from genome and transcriptome of 4 pigmented and two white rice varieties.
  5. Annotated SNPs from genome and transcriptome of 4 pigmented and two white rice varieties.
  6. Panel SNPs of pigmented rice varieties developed using Sequenom MassARRAY.

Why do flavonoid and folate as a source of nutritional values in rice?

Flavonoids are known as potent antioxidant properties. The production of these antioxidant properties involves biosynthesis, regulation and transport of biosynthetic genes and transcription factors in the flavonoid biosynthetic pathways. Pigmented rice such as black and rice showed highly associated with antioxidant properties. Therefore, understanding the genetic basis of these pigmented rice varieties are essential to develop and improve rice varieties with high nutritional values.

Folate is a vitamin B9 and high abundance in green leaves. In contrast, staple foods such as rice, wheat and potato contain a low abundance of folates which insufficient to meet the folate recommended daily intake (RDI) of 400 milligram/day for an adult and 600 milligrams/day during pregnancy (Blancquaert et al. 2014). Folate deficiency in human has led to neural tube defect, megaloblastic anaemia, Alzheimer and malnutrition. Hence, the improvement of folate content in rice varieties are important to ensure that people eat rice with high nutritional values and overcome the malnutrition issues in developing countries.

How do I get the flanking sequences of SNPs?

SNPs primer flanking sequences will be given upon request. Kindly email to: rabiatul [at] mardi dot gov dot my.

How is MyNutRiceBase supported?

SNPs primer flanking sequences will be given upon request. Kindly email to: rabiatul [at] mardi dot gov dot my.

MyNutRiceBase is funded by MARDI and in collaboration with INBIOSIS, UKM.

How do I cite MyNutRiceBase?

A manuscript of this database is in progress for submission to Database Oxford. For now please use the URL for the citation purpose.

How can I contact MyNutRiceBase?

MyNutRiceBase team can be reached via this email: nr_rice@gmail.com

Disclaimers

  • Access to raw reads can be obtained from ENA database (https://www.ebi.ac.uk/ena) under accession numbers; ERR2831551, ERR2831550, ERR2831549, ERR2831548, ERR2431962.
  • Many of these genomes remain work in progress, please respect this and treat the data accordingly.
  • If you wish to contribute or collaborate, please get in touch with Dr. Norliza Abu Bakar (lizaab[at]mardi dot gov dot my) & Zeti Azura Mohamed Huseein (zzeti.hussein[at]ukm.edu.my )
  • Any use of the data must include an acknowledgement of the group and cite using the website URL.
  • We hope you find these data useful and are looking forward to hearing about how it assisted you in your analyses.